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Sample GSM363863 Query DataSets for GSM363863
Status Public on Jan 24, 2009
Title Pha-4 starved L1 input
Sample type SRA
 
Source name pha-4 transgenic worm OP37
Organism Caenorhabditis elegans
Characteristics strain: OP37
growth stage: L1
antibody: none
Treatment protocol Resuspend embryo or Lava stage samples in 1% formaldehyde solution. Place on a shaker (50-100 rpm) and incubate for 30 minutes at room temperature. Wash samples once with 100 mM Tris pH 7.5 (to quench excess formaldehyde), 2 times with M9 Buffer, and once with FA buffer supplemented with protease inhibitors. Store at -80C
Growth protocol Transgenic worms were routinelly grow on plates to obtain as many adults with embryos. Bleach to obtain embryos. Hatch overnight in M9 Buffer to obtain L1s. Wash L1s and put into 500 ml liquid media (S medium+1X PSN antibiotics and nystatin) and grow at 20 oC in an incubator shaking at 230 rpm. Add concentrated E Colifor food as necessary during growth. It takes around 2.5-3 days to obtain adults with embryos. Collect adults and bleach to obtain embryos. Spin down embryos at 3000 g for 3 minutes. Resuspend pellet (embryos) and wash 2 more times with M9 Buffer. For embryo stage samples continue with cross-linking steps. For L1 stage samples, After collect adults from liquid culture and bleach to obtain embryos, The embryos were hatched overnight in M9 Buffer without any food to obtain L1s. Continue with the same wash and cross-linking steps.
Extracted molecule genomic DNA
Extraction protocol Chromatin was sheared to 200-800 bp using a Branson sonifier microtip. Immunoprecipitated using the indicated antisera. DNA and transcription factor complex was pull down, reversed cross-linking, ligated the adaptors to ChIP DNA, sequenced (gel purified 150-350bp) using Illumina Genome Analyzer.
 
Library strategy ChIP-Seq
Library source genomic
Library selection ChIP
Instrument model Illumina Genome Analyzer
 
Description No ChIP just input DNA from the same preparation
Data processing Enriched peak regions corresponding to transcription factor binding sites were identified by first extending all the uniquely mapped tags reads to the averaged sequenced DNA fragment size ~200bps and then accumulated into fragment density signal maps. Peaks in these maps are identified by comparison to a computer simulated null model for each Mb of each chromosome (accounting for the variability in mappability of sequence tags across the C. elegans genome. For potential target regions the number of sequenced tags is compared against the normalized number of sequence tags overlapping the region from the matching Input DNA reference sample. Fold enrichment ratios are computed from the ratio of these two sets of counts for each regions as well as p-value using the cumulative distribution function for the binomial distribution. P-value are corrected for multiple hypothesis testing using a Benjamini-Hochberg correction factor and a false discovery rate threshold of 0.05 is imposed. (See Rozowsky et al. Submitted)
 
Submission date Jan 23, 2009
Last update date May 15, 2019
Contact name Flora Vaccarino
Organization name Yale University
Department Child Study Center
Lab Vaccarino
Street address 230 South Frontage Road
City New Haven
State/province CT
ZIP/Postal code 06520
Country USA
 
Platform ID GPL9309
Series (2)
GSE14545 Identification of transcription factor Pha-4 binding regions
GSE15628 RNA polymerase occupancy at embryonic stage and starved L1 stage in pha-4 transgenic worms
Relations
SRA SRX002676
BioSample SAMN00005996

Supplementary file Size Download File type/resource
GSM363863_Yale_pha4_L1_Input_eland_result_rep1_laneA_FC30L81AA_110308_s_5.txt.gz 306.3 Mb (ftp)(http) TXT
GSM363863_Yale_pha4_L1_Input_eland_result_rep1_laneB_FC30L81AA_110308_s_6.txt.gz 300.0 Mb (ftp)(http) TXT
GSM363863_Yale_pha4_L1_Input_eland_result_rep2_laneA_FC30L81AA_110308_s_7.txt.gz 335.9 Mb (ftp)(http) TXT
GSM363863_Yale_pha4_L1_Input_eland_result_rep2_laneB_FC30L81AA_110308_s_8.txt.gz 363.6 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Processed data provided as supplementary file
Processed data are available on Series record
Raw data are available in SRA

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